[Bioperl-l] needle parser in bioperl?

Brian Osborne bosborne11 at verizon.net
Tue Dec 12 11:51:05 EST 2006


EMBOSS' needle and water produce alignments in what Bioperl calls 'emboss'
format, so you can use AlignIO to get SimpleAlign objects. The best
description of how to use SimpleAlign is the documentation in the module.

Brian O.

On 12/12/06 7:14 AM, "neeti somaiya" <neetisomaiya at gmail.com> wrote:

> Hi,
> Does anyone know of a bioperl parser for needle output, basically I won't
> where the target sequence aligns on the template (i.e. coordinate on the
> template where the taget aligns).

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